Nucleic acid fragments and specific detection method by molecular identification of different bacteria species of the genus Acinetobacter

ABSTRACT

RpoB gene sequences of various species of  Acinetobacter  bacteria, and a method of detection by molecular identification of various species of  Acinetobacter  bacteria using rpoB gene sequences.

The present invention relates to the area of diagnosis. More precisely, the invention concerns a method for the molecular identification of bacteria of the genus Acinetobacter using nucleic acid amplifying and sequencing techniques with oligonucleotide primers.

Bacteria of the genus Acinetobacter are bacteria appearing in the form of Gram-negative cocco-bacilli, having aerobic growth. Currently almost 60 species are known and 2 sub-species.

These bacteria are essentially, but not solely, agents of nosocomial infection. Their spectrum ranges from mere colonization to life-threatening infections, in particular pneumonia, urinary infection, bacteraemia and meningitis (van Dessel et al., 2004). Their excellent survival capacity in the external hospital environment and their ability to develop rapid resistance to most antibiotics are major factors in their emergence as agents of nosocomial infections, in particular in intensive care units (Bergogne-Berezin and Towner, 1996; Towner, 1997).

Although most species are responsible for infections in man, some species have only been isolated in the environment (Nemec et al., 2001, 2003; Carr et al., 2003).

Whereas in the genus Acinetobacter, 32 species have been proposed (van Dessel et al, 2004), 24<<genomic species>> according to nomenclature currently in force and abbreviated below to <<genospecies>> or <<g.sp.>>) are recognized and only 17 species have a validated name (Nemec et al., 2003; Carr et al., 2003). Unfortunately, the members of this genus have very broad intra-specific phenotype variability, and therefore cannot be differentiated at phenotype level. The increase in the number of infections related to these agents has prompted research into analysis methods for the identification and taxonomy of these bacteria. It has therefore been shown that identification methods based on phenotypical characteristics and sequencing of the 16S ribosomal RNA gene by comparison with DNA-DNA hybridisation are not valid. Therefore the search for rapid identification methods of these bacteria is still an issue (Gerner-Smidt et al., 1991; Ibrahim et al., 1997; Rainey et al., 1994). In particular, molecular techniques based on sequencing of the 16S ribosomal RNA gene do not allow a distinction to be made between the closest species, in particular due the lack of polymorphism of this gene within this genus. (Yamamoto and Harayama, 1998; Ochman and Wilson, 1987; Stackebrandt and Goebel, 1994). Additionally, owing to this lack of polymorphism, there is a need to determine the complete sequence of the 16S rRNA gene if it is wished to be able to identify a species. This requires sequencing the entirety of the gene which has around 1600 base pairs. The practical consequence is that sequencing must be based on a minimum of 6 sequencing reactions in addition to the amplification reaction to obtain an assessable result. Phylogenetic attempts have been made using the comparison of gyrB genes (Yamamoto and Harayama, 1996; Yamamoto et al., 1999) and recA genes (Krawczyk et al., 2002) as an alternative to the 16S ribosomal RNA gene (Ibrahim et al., 1997). Unfortunately, the sequences of these genes have not been determined on the 10 most recent species (Nemec et al., 2001, 2003; Carr et al., 2003).

There is therefore still a demand for a molecular identification tool to identify the bacteria species of genus Acinetobacter, which can be routinely used in bacteriology laboratories, in particular having a sufficiently polymorphic gene so that the determination of a short sequence (less than 500 base pairs) with only 1 amplification reaction and two sequence reactions is identifying i.e. can be amplified and sequenced using a single set of primers.

The inventors have discovered and shown according to the present invention that:

-   -   the rpoB gene and its non-coding boundary sequences, namely     -   the non-coding sequences at 5′ between the sequences of the rp/L         and rpoB genes (called “rplL-rpoB spacers” or <<rp/L-rpoB         intergenic fragments>> below), and     -   the non-coding sequences at 3′ between the sequences of the rpoC         and rpoB genes (called “rpoB-rpoC spacers” or <<rpoB-rpoC         intergenic fragments>> below),

form a genetic marker allowing the detection and specific identification of the bacterium of each species of genus Acinetobacter, and in particular of the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus.

The genomic species 1 to 16 (“genomic species>>) correspond to strains referenced in GENBANK, for some of which (no 3, 6, 9, 10, 13 and 16) no name has yet been given.

The inventors have discovered some hypervariable regions between the different species and hence specific to each species, flanked by conserved sequences between the different species, which can be used to implement a molecular identification method of the different species of Acinetobacter bacteria by amplification, using primers chosen from the conserved sequences and hybridisation and/or sequencing of the specific sequences so amplified.

More particularly, the present invention concerns sequences of nucleic acids specific to each species of genus Acinetobacter cited above whose nucleotide sequence is drawn from the rpoB gene of said bacteria.

According to Lazcano et al. [J. Mol. Evol. (1988) 27:365-376], the RNA polymerases are divided into two groups according to their origin, one consisting of RNA- or DNA-dependent viral RNA polymerises, and the other of DNA-dependent RNA polymerases of eukaryote or prokaryote origin (archaebacteria and eubacteria). The eubacterial, DNA-dependent RNA polymerases are characterized by a simple, conserved, multimeric constitution called a “core enzyme”, represented by αββ′, or “holoenzyme” represented by αββ′σ [Yura and Ishihama, Ann. Rev. Genet. (1979) 13:59-97]. Numerous studies have evidenced the functional role, within the multimeric enzymatic complex, of the β subunit of the eubacterial RNA polymerase. On the other hand, the archaebacterial, eukaryote RNA polymerases have a more complex structure which may reach around ten, even thirty subunits [Pühlet et al. Proc. Natl. Acad. Sci. USA (1989) 86:4569-4573].

The genes encoding the different αββ′σ subunits of DNA-dependent RNA polymerase in eubacteria, respectively the rpoA, rpoB, rpoC and rpoD genes, are classified in different groups comprising the genes coding for constituent proteins of the ribosomal subunits or for enzymes involved in the replication and repair of the genome [Yura and Yshihma, Ann. Rev. Genet. (1979) 13:59-97]. Some authors have shown that the sequences of the rpoB and rpoC genes could be used to construct phylogenetic trees [Rowland et al. Biochem. Soc. Trans. (1992) 21:40 S] allowing separation of the different branches and sub-branches of the living kingdoms.

Before setting forth the invention in detail, different terms used in the description and claims are defined as follows:

-   -   by “nucleic acid extracted from bacteria” is meant either the         total nucleic acid, or the genomic DNA, or the messenger RNAs,         or the DNA obtained from reverse transcription of the messenger         RNAs;     -   “nucleotide fragment” or “oligonucleotide” are two synonymous         terms designating a chain of nucleotide patterns characterized         by an information sequence of the natural (or possibly modified)         nucleic acids and able to hybridise, like the natural nucleic         acids, with a complementary or substantially complementary         nucleotide fragment, under predetermined high-stringency         conditions. The chain may contain nucleotide patterns having a         different structure to that of the natural nucleic acids. A         nucleotide fragment (or oligonucleotide) may for example contain         up to 100 nucleotide patterns. It generally contains at least         10, preferably from 18 to 35 nucleotide patterns and can be         obtained from a natural nucleic acid molecule and/or by genetic         recombination and/or by chemical synthesis,     -   a nucleotide pattern is derived from a monomer which may be a         natural nucleotide of nucleic acid whose constituent elements         are a sugar, a phosphate group and a nitrogen-containing base         chosen from among adenine (A), guanine (G), uracil (U), cytosine         (C), thymine (T); or else the monomer is nucleotide of which at         least one of the three previous constituent elements is         modified; for example the modification may concern a base, with         modified bases such as inosine which can hybridise with any base         A, T, U, C or G, methyl-5-deoxycytidine, deoxyuridine,         dimethylamino-5-deoxyuridine or any other modified base capable         of hybridisation either at the sugar e.g. the replacement of at         least one deoxyribose by a polyamide [Nielsen P E et al.,         Science (1991) 254:1497-1500], or at the phosphate group e.g.         through replacement by esters chosen in particular from among         the diphosphates, alkylphosphonates and phosphorothioates,     -   by “hybridisation”, is meant the process during which, under         suitable conditions, two nucleotide fragments having         sufficiently complementary sequences are able to combine under         stable specific hydrogen bonds to form a double strand. The         hybridisation conditions are determined by “stringency”, i.e.         the strictness of operating conditions. Hybridisation is all the         more specific the higher the stringency under which it is         conducted. Stringency is related in particular to the base         composition of a probe/target duplex, and to the extent of         mismatch between two nucleic acids. Stringency may also be         related to parameters of the hybridisation reaction, such as         concentration and the type of ion species present in the         hybridisation solution, the type and concentration of denaturing         agents and/or hybridisation temperature. The stringency of the         conditions under which a hybridisation reaction must be         performed depends in particular on the probes used. All these         data items are well known and the suitable conditions can         possibly be determined in each case by routine experiments. In         general, depending on the length of the probes used, the         temperature for the hybridisation reaction lies between         approximately 20 and 65° C., in particular between 35 and 65° C.         in a saline solution at a concentration of approximately 0.8 to         1 M.     -   a “probe” is a nucleotide fragment having hybridisation         specificity under determined conditions to form a hybridisation         complex with a nucleic acid having, in the present case, a         nucleotide sequence included either in a messenger RNA, or in a         DNA obtained by reverse transcription of said messenger RNA, a         transcription product; a probe may be used for diagnostic         purposes (capture or detection probes in particular) or for         therapeutic purposes,     -   a probe may be immobilized or able to immobilized on a solid         support by any suitable means, e.g. by covalency, by adsorption,         or by direct synthesis on a solid. Examples of supports comprise         microtitration plates and DNA chips,     -   a “probe” is generally labelled with a marking agent chosen for         example from among radioactive isotopes, enzymes, in particular         enzymes able to act on a chromogenic, fluorigenic or luminescent         substrate (in particular a peroxydase or an alkaline         phosphatase), or from among chromophorous chemical compounds,         chromogenic, fluorigenic or luminescent chemical compounds,         analogs of nucleotide bases. This marking may be direct between         the DNA and said marker, or indirect i.e. via ligands such as         biotin or other molecule able to bind to markers,     -   a “species probe” is a probe allowing specific identification of         the species of a bacterium of a given genus, Acinetobacter in         this case,     -   a “genus probe” is a probe allowing specific identification of         the genus of the bacterium, irrespective of the species of the         bacterium of said genus, under certain hybridisation conditions,     -   a “primer” is a probe comprising for example 10 to 100         nucleotide patterns and having hybridisation specificity under         determined conditions for enzymatic amplification reactions,     -   by “genus primer”, is meant a set of primers allowing specific         amplification of any bacterium of one same given genus, with no         distinction as to species, under certain hybridisation and         amplification conditions (the “genus primers” are also called         “consensus primers” or “universal primers” in the present         application),     -   by “amplification reaction” is meant an enzymatic polymerisation         reaction, e.g. in an amplification technique such as PCR,         initiated by primer oligonucleotides and using a DNA polymerase,     -   by “sequencing reaction”, is meant a reaction leading to         determination of the sequence of a nucleic acid fragment, or of         a complete gene by an abortive polymerisation process starting         with oligonucleotide primers and using said dideoxynucleotides         (Sanger F, Coulson A R (1975), J. Mol. Biol. 94: 441) or by         multiple hybridisations with multiple probes fixed onto a solid         support such as used in DNA chips for example, or other         techniques known to those skilled in art.

The inventors have determined the complete sequences of the rpoB genes and their non-coding boundary sequences separating them from the rp/L and rpoC genes (“rplL-rpoB spacer” and “rpoB-rpoC spacer”) of 24 species of the genus Acinetobacter. A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus.

To arrive at determining said complete sequences of rpoB and its flanking sequences in all the species of Acinetobacter bacteria, the inventors after a large number of unsuccessful tests and from the sole rpoB sequence and its non-coding boundary regions in bacteria of genus Acinetobacter—were firstly compelled to determine 51 primers (Table 2) of corresponding sequences of bacteria which they identified as being close and available from GENBANK, namely Acinetobacter sp. ADP1 (GenBank accession number NC_(—)005966), Pseudomonas syringae pv. tomato str.DC3000 (GenBank accession number NC_(—)004578) and P. putida KT2440 (GenBank accession number NC_(—)006347).

Acinetobacter strain sp. ADP1 is a strain which had not been characterized before the invention, and which does not correspond to any of the pathogenic strains described in the present patent application and listed below.

The subject-matter of the present invention is therefore a complete rpoB gene of a bacterium of the genus Acinetobacter chosen from among the following 23 species: A. calcoaceticus (genomic species 1), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence comprises and more particularly consists of a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 9 and 11 to 32 respectively, and the sequences having at least 98% similarity, and their complementary sequences.

A further subject of the present invention concerns nucleic acid fragments comprising and more particularly consisting of a non-coding fragment flanking the rpoB gene of a bacterium of the genus Acinetobacter chosen from among the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence comprises and more particularly consists of a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 121 to 144 respectively, and sequences SEQ. ID. no 165 to 188 respectively, and the sequences having at least 98% similarity and their complementary sequences.

The said sequences having similarity rates of at least 98% with said sequences SEQ. ID. 9 to 32, 121 to 144 and 165 to 188 correspond to the possible variations between the different strains of one same species possibly corresponding to sub-species. Therefore sequences SEQ. ID. no 145 to 164 and 189 to 208 correspond to various strains of A. baumannii having at least 98% homology with sequences SEQ. ID. no 122 and 166 respectively.

By “similarity rate” or “homology percentage”, is meant a percentage of sequence identity i.e. a percentage of nucleotides of the sequences which are identical at the same position with respect to another sequence.

Sequences SEQ. ID. no 121 to 144 correspond to the 5′ flanking sequences representing the complete rpoB spacer bordering the rpoB gene between genes rp/L and rpoB, having a length of between 301 and 310 bp, for each species of the bacterium of the genus Acinetobacter, in the 24 above-mentioned species.

Sequences SEQ. ID. no 165 to 188 correspond to 3′ flanking sequences representing the complete rpoB-rpoc spacer bordering the rpoB gene between the rpoB and rpoC genes, having a length of between 86 and 177 bp, for each species of the bacterium of genus Acinetobacter, in the 24 above-mentioned species.

The spacers rpoB-rpoC and rp/L-rpoB which border the rpoB gene, and the complete sequence of the rpoB gene can be used to identify the bacterium not only as probe and/or by investigating its primary sequence, but also by investigating the secondary and tertiary structures of the messenger RNA derived from transcription of the complete DNA sequence.

In these rpoB genes and their non-coding boundary sequences (rplL-rpoB spacer and rpoB-rpoC spacer) of Acinetobacter, the inventors have evidenced consensus sequences SEQ. ID. no 1, 2, 3, 4, 5, 6, 7 and 8 (Table 3) which are conserved sequences between all bacteria of the genus Acinetobacter, i.e. able to be used as primers to amplify the same portion of the rpoB gene and its non-coding boundary regions (rp/L-rpoB spacer and rpoB-rpoC spacer) of all said Acinetobacter bacteria, namely:

-   -   SEQ. ID. no 1, and 2 for a first region of the rpoB gene,     -   SEQ. ID. no 3, and 4 for a second region of the rpoB gene,     -   SEQ. ID. no 5, and 6 for the rp/L-rpoB spacer and     -   SEQ. ID. no 7, and 8 for the rpoB-rpoC spacer,     -   SEQ. ID. no 1 to 4 and 6-7 lie inside the rpoB gene, with:     -   SEQ. ID. no 8 and 6 are close to the 5′ ends of the rpoB and         rpoC genes respectively,     -   SEQ. ID. no 7 and 5 are close to the 3′ ends of the rp/L and         rpoB genes respectively.

The present invention therefore provides oligonucleotides which have conserved sequences of an Acinetobacter bacterium chosen from among the said 24 species comprising a sequence of at least 12, preferably at least 18 consecutive nucleotide patterns included in one of the sequences chosen from the sequences such as described in following sequences SEQ. ID. no 1 to 8, and their complementary sequences, and preferably consisting of said sequences:

SEQ ID NO: 1: 5′-TAYCGYAAAGAYTTGAAAGAAG-3′, SEQ ID NO: 2: 5′-CMACACCYTTGTTMCCRTGA-3′, SEQ ID NO: 3: 5′-GTGATAARATGGCBGGTCGT-3′, SEQ ID NO: 4: 5′-CGBGCRTGCATYTTGTCRT-3′, SEQ ID NO: 5: 5′-GAAGARCTTAAGAMDAARCTTG-3′ SEQ ID NO: 6: 5′-CGTTTCTTTTCGGTATATGAGT-3′, SEQ ID NO: 7: 5′-GTTCTTTAGGTATCAACATTGAA-3′, SEQ ID NO: 8: 5′-GACGCAAGACCAATACGRAT-3′,

in which:

-   -   D represents A, G or T,     -   Y represents C or T,     -   B represents C, G or T,     -   R represents A or G, and     -   M represents A or C.

At the position corresponding to a nucleotide D, Y, B, M or R in sequences SEQ. ID. no 1 2, 3, 4, 5 and 8, variable nucleotides are found in the complementary target sequences in relation to the species of bacterium under consideration, but all the other nucleotides are conserved in all the species of bacteria of the genus Acinetobacter.

Sequences SEQ. ID. no 1, 3, 5 and 7 are used as primers on the direct strand, and sequences SEQ. ID. no 2, 4, 6 and 8 are used as primer on the indirect strand. Sequences SEQ. ID. no 2, 4, 6 and 8 therefore correspond to sequences complementary to those of the direct strand.

To be used as consensus primers, these oligonucleotides of sequences SEQ. ID. no 1, 2, 3, 4, 5 and 8 are therefore used in the form of equimolar mixtures of oligonucleotides of different sequences, said oligonucleotides of different sequences for each sequence SEQ. ID. no 1 to 8 meeting the various possible definitions of respective sequences no 1, 2, 3, 4, 5 and 8.

These equimolar mixtures of oligonucleotides are obtained through the use, during oligonucleotide synthesis, of equimolar mixtures of the different nucleotides concerned, respectively:

-   -   A, G and T for D,     -   C and T for Y,     -   C, G and T for B,     -   A and G for R,     -   A and C for M.

The mixtures of oligonucleotides, meeting the definition nucleotides of sequences SEQ. ID. no 1 2, 3, 4, 5 and 8, are therefore able to hybridise with the different target complementary sequences included in the rpoB genes and at the ends of the rp/L and rpoC genes flanking their boundary non-coding regions (rplL-rpoB spacer and rpoB-rpoC spacer) of all the species of bacteria of the genus Acinetobacter and, more particularly, the 24 above-mentioned species.

The capacity of these primers to amplify rpoB gene fragments and their non-coding boundary regions (rplL-rpoB spacer and rpoB-rpoC spacer), of all species of Acinetobacter, allows the consideration to be made that these primers will be efficient in identifying additional species of Acinetobacter which may be described in the future.

A further subject of the invention is therefore a mixture of oligonucleotides characterized in that it comprises an equimolar mixture of oligonucleotides of different sequences comprising at least 12, preferably at least 18 consecutive nucleotide patterns included in one of sequences SEQ. ID. no 1 to 5 and 8, or the oligonucleotides of complementary sequences.

More particularly, the subject of the present invention is the following mixtures of oligonucleotides:

-   -   an equimolar mixture of 8 oligonucleotides of different         sequences, consisting of sequence SEQ. ID. no 1 or         oligonucleotides of complementary sequences.     -   an equimolar mixture of 16 oligonucleotides of different         sequences, consisting of sequence SEQ. ID. no 2 or         oligonucleotides of complementary sequences.     -   an equimolar mixture of 6 oligonucleotides of different         sequences, consisting of sequence SEQ. ID. no 3 or         oligonucleotides of complementary sequences.     -   an equimolar mixture of 24 oligonucleotides of different         sequences, consisting of sequence SEQ. ID. no 4 or         oligonucleotides of complementary sequences.     -   an equimolar mixture of 24 oligonucleotides of different         sequences, consisting of sequence SEQ. ID. no 5 or         oligonucleotides of complementary sequences.     -   sequence oligonucleotide consisting of sequence SEQ. ID. no 6 or         a complementary sequence.     -   sequence oligonucleotide consisting of sequence SEQ. ID. no 7 or         a complementary sequence.     -   an equimolar mixture of 2 oligonucleotides of different         sequences consisting of sequence SEQ. ID. no 8 or         oligonucleotides of complementary sequences.

The oligonucleotides or mixtures of oligonucleotides comprising a sequence included in one of sequences SEQ. ID. no 1 to 8 according to the invention, can be used as genus primers for bacteria of the genus Acinetobacter.

As mentioned previously, the consensus sequences SEQ. ID. no 1, 2, 3, 4, 5 and 8, so defined, also flank hypervariable sequences whose sequence is specific to each species of the genus Acinetobacter.

The inventors were therefore able to evidence sequences specific to species for each of the 24 above-cited bacteria species, corresponding to sequences:

-   -   SEQ. ID. no 33 to 56, flanked by consensus sequences SEQ. ID. no         1 and 2 (hereafter “region 1 of rpoB”);     -   SEQ. ID. no 77 to 100, flanked by consensus sequences SEQ. ID.         no 3 and 4 (hereunder “region 2 of rpoB”);     -   SEQ. ID. no 121 to 144, flanked by consensus sequences SEQ. ID.         no 5 and 6 (hereunder “rpo/L-rpoB spacer”); and     -   SEQ. ID. no 165 to 188, flanked by consensus sequences SEQ. ID.         no 7 and 8 (hereunder “rpoB-rpoC spacer”);

The oligonucleotides of sequences flanked by SEQ. ID. no 1 2, 3, 4, 5, 6, 7 and 8, can therefore be used as species primer for bacteria of the genus Acinetobacter.

Said specific hypervariable sequences SEQ. ID. no 33 to 56 flanked by sequences SEQ. ID. no 1 and 2, represent a fragment of the rpoB gene of length 350 bp, with less than 96% similarity between the different species (Table 7) with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. junii, which means that they form a short specific target sequence for the specific identification of each species of the bacterium of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. junii.

Said specific hypervariable sequences SEQ. ID. no 77 to 100 flanked by sequences SEQ. ID. no 3 and 4, represent a fragment of the rpoB gene of length 450 bp with less than 96% similarity between the different species (Table 8) with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. junii, which means that they form a second short specific target sequence to specifically identify each bacterium species of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. juni.

Said specific hypervariable sequences SEQ. ID. no 121 to 164 flanked by sequences SEQ. ID. no 5 and 6, represent the rplL-rpoB spacer bordering the rpoB gene by a length of between 301 and 310 bp with less than 97% similarity between the different species (see Table 5 below) with the exception of the pairs A. baylii/genospecies 11, A. grimontii/A. junii, and A. lwoffi/genospecies 9, which means that they form a third short specific target sequence to specifically identify each bacterium species of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. baylii/genospecies 11, A. grimontii/A. junii, and A. lwoffi/genospecies 9.

Finally, said specific hypervariable sequences SEQ. ID. no 165 to 188 flanked by sequences SEQ. ID. no 7 and 8, represent the rpoB-rpoC spacer bordering the rpoB gene by a length of between 86 and 177 bp with less than 97% similarity between the different species (see Table 6 below) with the exception of the pairs A. grimontii/A. junii and species of the Acb group (A. baumannii, A. calcoaceticus and genospecies 3), so that they form a fourth short specific target sequence for the specific identification of each bacterium species of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. grimontii/A. junii and species of the Acb group (A. baumannii, A. calcoaceticus and genospecies 3).

A further subject of the present invention is therefore an rpoB gene fragment of a bacterium of genus Acinetobacter chosen from among the 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence consists of a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 33 to 56 respectively, and sequences SEQ. ID. no 77 to 100 respectively, and the sequences having at least 98% similarity and their complementary sequences.

A further subject of the present invention is an rpoB gene fragment of a bacterium of the genus Acinetobacter chosen from among the 23 species: A. calcoaceticus (genomic species 1), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence comprises a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 33 and 35 to 56 respectively, and sequences SEQ. ID. no 77 and 79 to 100 respectively, and the sequences having at least 98% similarity and their complementary sequences.

The said sequences having similarity rates of at least 98% with said sequences SEQ. ID. no 33 to 56 and 77 to 100 correspond to possible variations between the different strains of one same species, possibly and more particularly corresponding to sub-species. Therefore the sequences SEQ. ID. no 57 to 76 and 101 to 120 correspond to various strains of A. baumannii having at least 98% homology with SEQ. ID. no 34 and 78 respectively.

The subject of the present invention is therefore also the use, as species probe, of a rpoB, rp/L or rpoC gene fragment according to the invention or of an oligonucleotide of sequences specific to a said species of Acinetobacter bacterium according to the invention.

More precisely, the present invention provides a method of detection by molecular identification to identify a bacterium of one of the species of the genus Acinetobacter, characterized in that the following are used:

-   -   the complete rpoB gene of said bacterium according to the         invention, comprising a said sequence SEQ. ID. no 9 to 32, or         preferably consisting of a said sequence SEQ. ID. no 9 to 32, or         the complementary sequences, or sequences having at least 98%         similarity,     -   an rpoB gene fragment of a said bacterium according to the         invention, comprising a said sequence SEQ. ID. no 33 to 56 or 77         to 100, or consisting of a said sequence SEQ. ID. no 33 to 56 or         77 to 100, or the complementary sequences, or sequences having         at least 98% similarity,     -   an rpoB gene fragment of a said bacterium according to the         invention, comprising a said sequence SEQ. ID. no 77 to 100, or         preferably, consisting of a said sequence SEQ. ID. no 77 to 100,         or complementary sequences, or sequences having at least 98%         similarity,     -   a gene fragment comprising a complete rplL-rpoB or rpoB-rpoC         intergenic fragment of said bacterium according to the         invention, comprising a said sequence SEQ. ID. no 121 to 144 or         165 to 188, or preferably consisting of a said sequence SEQ. ID.         no 121 to 144 or 165 to 188, the complementary sequences or         sequences having at least 98% similarity,     -   an oligonucleotide having a sequence specific to an         Acinetobacter bacterium chosen from among the 24 above-cited         species, preferably with at least 18, further preferably 18 to         35 consecutive nucleotide patterns included in one of the         sequences chosen from among the sequences such as described in         sequences:     -   SEQ. ID. no 33 to 56 respectively,     -   SEQ. ID. no 77 to 100 respectively,     -   SEQ. ID. no 121 to 144 respectively,     -   SEQ. ID. no 165 to 188 respectively, and     -   the sequences having at least 98% similarity and their         complementary sequences, or     -   an oligonucleotide or equimolar mixture of oligonucleotides         according to the invention, comprising a sequence of at least         12, preferably 18 consecutive nucleotides included in one of         sequences SEQ. ID. no 1 2, 3, 4, 5, 6, 7 and 8 or their         complementary sequences, or preferably consisting of one of said         sequences SEQ. ID. no 1 2, 3, 4, 5, 6, 7 and 8.

In a first embodiment of a bacterium detecting method of the invention, it is sought specifically to detect a given species of an Acinetobacter bacterium chosen from among the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, a method in which:

1—a sample containing or likely to contain nucleic acids of at least one said bacterium is contacted with at least one species probe consisting of an oligonucleotide or gene fragment according to the invention, preferably a gene fragment respectively consisting of one of said sequences chosen from among:

-   -   SEQ. ID. no 33 to 56 respectively,     -   SEQ. ID. no 77 to 100 respectively,     -   SEQ. ID. no 121 to 144 respectively,     -   SEQ. ID. no 165 to 188 respectively, and     -   the sequences having at least 98% similarity and their         complementary sequences.

2—the formation or non-formation of a hybridisation complex is determined between said probe and the nucleic acids of the sample, and it is thereby determined whether said species of Acinetobacter is present in the sample if a hybridisation complex is formed.

In a second embodiment of a method to detect a specific species of a bacterium of the genus Acinetobacter, the steps are performed in which:

1—amplification primers comprising said mixtures of oligonucleotides of the invention are contacted with a sample containing or likely to contain nucleic acids of at least one said bacterium of the genus Acinetobacter, and nucleic acid amplification is performed by enzymatic polymerisation reaction comprising:

-   -   as 5′ primer, at least one oligonucleotide or mixture         oligonucleotides according to the invention comprising a         sequence included in one of sequences SEQ. ID. no 1, 3, 5 and 7,         preferably consisting of said complete sequence SEQ. ID. no 1,         3, 5 and 7 or the complementary sequences, and     -   as 3′ primer, at least one oligonucleotide or mixture of         oligonucleotides according to the invention comprising sequences         included in one of sequences SEQ. ID. no 2, 4 6, and 8         respectively, preferably consisting of said complete sequence         SEQ. ID. no 2, 4, 6, and 8, or respectively a complementary         sequence.

2—and the formation or non-formation of an amplification product is determined, and the presence of absence of said bacterium in the sample is thereby respectively determined if an amplification product is or is not formed.

More particularly, it is sought to determine a given species of an Acinetobacter bacterium chosen from among the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, and, at step 2 above, the presence or absence of the given species of a said bacterium is determined by conducting the steps in which:

a) a sequencing reaction is conducted of a gene fragment is amplified with said primers, and

b) the sequence of said amplified fragment obtained is compared with the sequence of a gene fragment of said bacterium respectively comprising:

-   -   said sequences SEQ. ID. no 33 to 56, when said 5′ and 3′ primers         are oligonucleotides of sequences included in sequences SEQ. ID.         no 1 and 2 respectively,     -   said sequences SEQ. ID. no 77 to 100, when said 5′ and 3′         primers are oligonucleotides of sequences included in sequences         SEQ. ID. no 3 and 4 respectively, and     -   said sequences SEQ. ID. no 121 to 144, when said 5′ and 3′         primers are oligonucleotides of sequences included in sequences         SEQ. ID. no 5 and 6 respectively, and     -   said sequences SEQ. ID. no 165 to 188, when said 5′ and 3′         primers are oligonucleotides of sequences included in sequences         SEQ. ID. no 7 and 8 respectively.

In another variant of said second embodiment of a method to detect a specific species of a bacterium of the genus Acinetobacter, it is sought to detect a specific species of an Acinetobacter bacterium chosen from among the 24 following species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, and at step 2 above the presence or absence of the given species of said bacterium is determined by conducting the steps in which:

a—a sample containing or likely to contain amplified nucleic acids of at least one said bacterium is contacted with at least one species probe consisting of an rpoB gene fragment or a specific oligonucleotide of the invention, preferably a fragment consisting respectively of one of said sequences chosen from among:

-   -   SEQ. ID. no 33 to 56 respectively, when said 5′ and 3′ primers         are oligonucleotides of sequences included in sequences SEQ. ID.         no 1 and 2 respectively,     -   SEQ. ID. no 77 to 100 respectively, when said 5′ and 3′ primers         are oligonucleotides of sequences included in sequences SEQ. ID.         no 3 and 4 respectively, and     -   SEQ. ID. no 121 to 144 respectively, when said 5′ and 3′ primers         are oligonucleotides of sequences included in sequences SEQ. ID.         no 5 and 6 respectively, and     -   SEQ. ID. no 165 to 188 respectively, when said 5′ and 3′ primers         are oligonucleotides of sequences included in sequences SEQ. ID.         no 7 and 8 respectively, and

b—the formation or non-formation of a hybridisation complex is determined between said probe and the amplified nucleic acids of the sample, and the presence or absence in the sample of said species of Acinetobacter is thereby determined according to whether or not a hybridisation complex is formed.

In one preferred embodiment of a method according to the invention, the steps are performed comprising:

1—a first amplification of the nucleic acid of said sample with a pair of 5′ and 3′ primers chosen from among said mixtures of oligonucleotides of the invention, comprising sequences respectively included in sequences SEQ. ID. no 1 and SEQ. ID. no 2, preferably consisting of said sequences SEQ. ID. no 1 and 2, or the complementary sequences, and

2—a first determination of the onset or absence of an amplification product containing the nucleic acids of at least one said bacterium, by hybridisation or optionally sequencing, and comparison of the amplicons obtained at step 1 with the fragments respectively consisting of one of said sequences chosen from among SEQ. ID. no 33 to 56 and 34 to 76 respectively, and

-   -   if, at this step 2, the presence of species A. grimontii or A.         junii is determined, the following is also performed:

3a—a second amplification reaction with avec 5′ and 3′ primers chosen from among said oligonucleotide mixtures according to the invention, comprising sequences respectively included in sequences SEQ. ID. no 3 and SEQ. ID. no 4, preferably consisting of said sequences SEQ. ID. no 3 and 4, or the complementary sequences, and

4a—determining the formation or non-formation of an amplification product containing nucleic acids of at least one said bacterium, by hybridisation or optionally sequencing, and comparing the amplicons obtained at step 3a with the fragments respectively consisting of one of said sequences chosen from among SEQ. ID. no 77 to 100 respectively, or

-   -   if, at first step 2, the presence of species A. baylii or         genomic species 11 is determined, the following is also         performed:

3b—a second amplification reaction with 5′ and 3′ primers chosen from among said mixtures of oligonucleotides according to the invention containing sequences respectively included in sequences SEQ. ID. no 7 and SEQ. ID. no 8, preferably consisting of said sequences SEQ. ID. no 7 and 8, or the complementary sequences, and

4b—determining the formation or non-formation of an amplification product containing nucleic acids of at least one said bacterium, by hybridisation or optionally sequencing, and comparison of the amplicons obtained at step 3b with the fragments respectively consisting of one of said sequences chosen from among SEQ. ID. no 165 to 188 respectively.

Sequences SEQ. ID. no 1 to 208 can be prepared by genetic engineering and/or by automatic synthesis or chemical synthesis using techniques well known to those skilled in the art.

The probes of the invention can be used for diagnostic purposes, as mentioned above, by determining the formation or non-formation of a hybridisation complex between the probe and a target nucleic acid in a sample, using any known hybridisation technique and in particular so-called “DOT-BLOT” techniques [Maniatis et al. (1982) Molecular Cloning, Cold Spring Harbor], DNA transfer techniques called “SOUTHERN BLOT” [Southern E. M., J. Mol. Biol. (1975) 98:503], RNA transfer techniques called “NORTHERN BLOT”, or so-called “sandwich” techniques, in particular with a capture probe and/or detection probe, said probes being able to hybridise with two different regions of the target nucleic acid, and at least one of said probes (generally the detection probe) being able to hybridise with a target region specific to the species, on the understanding that the capture probe and the detection probe must have nucleotide sequences that are at least partly different.

The nucleic acid to be detected (target) may be DNA or RNA (the first obtained after PCR amplification). When detecting a target of double strand nucleic acid type, this acid must be denatured before initiating the detection method. The target nucleic acid may be obtained by extraction using known methods for nucleic acids of a sample to be tested. The denaturing of a double strand nucleic acid can be performed using known chemical, physical or enzymatic denaturing methods, in particular by heating to a suitable temperature of more than 80° C.

To implement the above-cited hybridisation techniques, in particular the “sandwich” techniques, a probe of the invention, called a capture probe, is immobilized on a solid support, and another probe of the invention, called a detection probe, is labelled with a marking agent. The examples of support and marking agent are as previously defined.

Advantageously, one species probe is immobilized on a solid support, and another species probe is labelled with a marking agent.

Another application of a said mixture of oligonucleotides of the invention is its use as nucleotide primer comprising a monocatenary oligonucleotide chosen from among oligonucleotides having a sequence of at least 12 nucleotide patterns included in one of sequences SEQ. ID. no 1 to 8, which can be used for the synthesis of a nucleic acid in the presence of a polymerase using a method known as such, in particular in amplification methods using said synthesis in the presence of a polymerase (PCR, RT-PCR, etc.). In particular, a primer of the invention can be used for the specific reverse transcription of a messenger RNA sequence of a bacterium species of the genus Acinetobacter, to obtain a corresponding complementary DNA sequence. Said reverse transcription may form the first stage of the RT-PCR technique, the following stage being PCR amplification of the complementary DNA obtained.

In one particular case, said primer comprising an oligonucleotide of the invention also comprises the sense or anti-sense sequence of a promoter recognized by an RNA polymerase (promoters T7, T3, SP6 for example [Studier F W, B A Moffatt (1986) J. Mol. Biol. 189:113]: said primers can be used in nucleic acid amplification methods involving a transcription step such as, for example, NASBA or 3SR techniques [Van Gemen B. et al. Abstract MA 1091, 7^(th) International Conference on AIDS (1991) Florence, Italy].

A further subject of the invention is a nucleotide primer comprising a mixture of monocatenary oligonucleotides chosen from among the oligonucleotides having sequences comprising one of sequences SEQ. ID. no 1 to 8 or preferably consisting of one of sequences SEQ. ID. no 1 to 8, which can be used for total or partial sequencing of the rpoB gene or of the rplL-rpoB spacer or rpoB-rpoC spacer of any species of the genus Acinetobacter.

The sequencing of the complete or partial rpoB gene or of the rplL-rpoB spacer or rpoB-rpoC spacer in any bacterium of the genus Acinetobacter allows the identification of any Acinetobacter bacterium by bio-computerized analysis of this sequence and allows the recognition of new species of unknown Acinetobacter bacteria.

Preferably, for use as primer or to sequence the rpoB genes or the rplL-rpoB spacer or rpoB-rpoC spacer, said mixtures of oligonucleotides of sequence SEQ. ID. no 1 and 2 are used.

A further subject of the present invention is a diagnosis kit which can be used in a method of the invention, containing at least one said rpoB gene fragment or rplL-rpoB spacer or rpoB-rpoC spacer according to the invention, comprising or consisting of one of sequences SEQ. ID. no 9 to 188 or an oligonucleotide or said equimolar mixture of oligonucleotides according to the invention, comprising sequences included in sequences SEQ. ID. no 1 to 8 and the oligonucleotides and rpoB gene fragments or rplL-rpoB spacer or rpoB-rpoC spacer of complementary sequences such as defined above, and, preferably, reagents which can be used for hybridisation reactions or amplification reactions or for sequencing accordingly.

As mentioned in the definitions, an oligonucleotide or nucleic acid fragment according to the invention, may be in the form of a deoxyribonucleic acid (DNA) or a ribonucleic acid (RNA) for which T is replaced by U in this case.

Finally, a last subject of the invention is a gene therapy probe to treat infections caused by a strain belonging to a species of the genus Acinetobacter, said probe comprising an oligonucleotide such as defined previously. This gene therapy probe, able to hybridise on the messenger RNA and/or on the genomic DNA of said bacteria, is able to block phenomena of translation and/or transcription and/or replication.

The principle of gene therapy methods is known and is based in particular on the use of a probe corresponding to an anti-sense strand: the formation of a hybrid between the probe and the sense strand is capable of disturbing at least one of the decoding steps of genetic data. Gene therapy probes can therefore be used as antibacterial medicinal products, to combat infections caused by bacteria species of the genus Acinetobacter.

Other characteristics and advantages of the present invention will become apparent and the invention will be better understood with the help of the description given below of the experiments conducted to implement the invention, together with their results, which are given solely by way of illustration.

Table 1, below, reproduces the list of species of Acinetobacter for which rpoB sequences and the rplL-rpoB spacer and rpoB-rpoC spacer were determined, the mentioned strains were obtained from the collection Collection de l'Institut Pasteur (CIP), sequences SEQ. ID. no 1 to 208 are described in the sequence listing appended to the description.

Table 2 lists the different primers used for amplification and sequencing of the rpoB genes.

When Table 2 gives sequences comprising nucleotides W, H, Y, V, R, B, M, K, S or D, these have the meanings known to persons skilled in the art, and in equally conventional fashion these primers are used in the form of an equimolar mixture of oligonucleotides of different sequences in the place of said nucleotides as explained above.

Table 3 gives comparisons of similarities of the sequences of the 16S rRNA and rpoB genes between the two sub-species C. affermentans and between the 11 pairs of species considered as close for which similarities between sequences of 16S rRNA genes are 98.5% or over, with a statistical comparison of the mean similarities obtained.

FIG. 1 is a graphical representation of the variability rate (range site variability: RSV (Y axis)) of the sequences of the rpoB genes and flanking sequences of the different species of genus Acinetobacter investigated per window of 50 nucleotides (X axis). The hypervariable regions, bounded by the conservative regions and used for species identification using consensus primers, are boxed.

FIG. 2 is a dendogram showing the phylogenetic relationships between the different species of Acinetobacter using the “neighbour-joining” method. The tree was constructed by aligning sequences of the rpoB gene. “Bootstrap” sampling values (percentage probability of node accuracy) calculated on the basis of a sample of 1000 trees, are given at each node, only values of 75% or higher being indicated.

FIG. 3 is a dendogram showing the phylogenetic relationships between different species of Acinetobacter using the “neighbour-joining” method. The tree was constructed by aligning hypervariable sequences (region 1 and region 2) of the rpoB gene. The “bootstrap” values (percentage probability of node accuracy) calculated on the basis of a sample of 1000 trees, are indicated at each node.

FIG. 4 is a dendogram showing the phylogenetic relationships between the different species of Acinetobacter using the “neighbour-joining” method. The 4 trees were constructed by aligning sequences of the rpoB, 16SRNA, rpoB, gyrB, recA genes. The “bootstrap” sampling values (percentage probability of node accuracy) calculated on the basis of a sample of 1000 trees, are given at each node, solely values of 75% or higher being indicated.

1—MATERIAL AND METHODS 1.1—Bacterial Strains

The bacterial strains used are listed in Table 1. All the strains were cultured on Columbia agar, 5% sheep blood, and were incubated 48 h at 37° C. under aerobic conditions.

1.2—Amplification and Sequencing of the rpoB Gene and of Spacers rplL-rpoB and rpoB-rpoC

The sequence of the rpoB gene and of its boundary intergenic spacers in the closest species were aligned to produce a consensus sequence. The sequences chosen were those of Acinetobacter sp. ADP1 (GenBank accession number NC_(—)005966), Pseudomonas syringae pv. tomato str.DC3000 (GenBank accession number NC_(—)004578) and P. putida KT2440 (GenBank accession number NC_(—)006347). The consensus sequence allowed determination of the primers subsequently used for PCR techniques, “genome walking” and sequencing. Some primers were determined after analysis of the results obtained. The primers are given in Table 2 below.

The bacterial DNA was extracted from strain suspensions using the QIAamp blood kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. All the PCR reaction mixtures contained 2.5×10⁻² U Taq polymerase per μl, 1× Taq buffer, 1.8 mM MgCl₂ (Gibco BRL, Life Technologies, Cergy Pontoise, France), 200 μM dATP, dCTP, dTTP and dGTP (Boehringer Manheim GmbH, Hilden, Germany), and 0.2 μM of each primer (Eurogentec, Seraing, Belgium). The PCR reaction mixtures were subjected to 35 denaturing cycles at 94° C. for 30 s, hybridisation of the primers for 30 s, and elongation at 72° C. for 2 min. Each amplification programme started with a denaturing step at 95° C. for 2 min. and ended with an elongation step at 72° C. for 10 min. Determination of the sequence of the gene ends was performed using the Universal GenomeWalker Kit (Clontech Laboratories, Palo Alto, Calif.). In short, genomic DNA was digested by Eco RV, Dra I, Pvu II, Stu I and Sca I. The DNA fragments were bound with the GenomeWalker adaptor, PCR was conducted by incorporating the “adaptor primer” provided by the manufacturer and the specific primers. For amplification, 1.5 U of ELONGASE enzyme (Boehringer Manheim) were used with 10 pmol of each primer, 20 mM of each dNTP, 10 mM Tris-HCl, 50 mM KCl, 1.6 mM MgCl₂ and 5 μl digested DNA for a final volume of 50 μl. The amplicons were purified with the “QIAquick spin PCR purification kit” (Qiagen). The sequence reactions were performed using reagents of the ABI Prism 3100 ADN sequencer (dRhod.Terminator RR Mix, Perkin Elmer Applied Biosystems).

These conditions for DNA extraction, PCR amplification and sequencing were described in Khamis et al 2003.

1.3—Determination of the Partial Discriminating Sequences in the rpoB Gene

To detect the sequence portions with high variability flanked by conserved regions, we used the SVARAP programme (Sequence VARiability Analysis Program). Once this analysis was made, the most polymorphic regions of the rpoB gene were determined and universal primers, chosen in the conserved boundary regions, were designated after different unsuccessful attempts. The PCR conditions incorporating the universal primers were the same as previously mentioned. These primers were used for amplification and sequencing of the 4 hypervariable regions for all the strains tested.

These primers are given in Table 3 below and FIG. 1.

1.4—Analysis of rpoB Sequences and their Boundary Intergenic Spacers

The fragments of rpoB gene sequences and of boundary intergenic spacers obtained in this study were analysed using “Sequence Analysis Software” (Applied Biosystems), and the partial sequences were combined into a single consensus sequence using “Sequence Assembler Software” (Applied Biosystems). All the deposit references of the strains with Collection de l'Institut Pasteur (<<CIP>>) (France, Paris) are listed in Table 1. The multiple alignments and similarity percentages between the genes of the different species were performed using CLUSTAL W on the EMBL-EBI server (Thompson et al. 1994). Phylogenetic trees were made from the sequences using the “neighbour—joining” method (Felsenstein et al. 1989). “Bootstrap” values were calculated to assess the solidity of the nodes, using SEQBOOT in PHYLIP software.

2—RESULTS a. Complete Sequences of the rpoB Genes of the Different Acinetobacter Species

The designated primers allowed amplification of the test regions in all working strains; the size of the complete gene is 4089 bp for all species. The similarity percentages between strains vary from 83 to 94%, with the exception of 2 pairs of species (Table 4). Two pairs of species A. junii/A. grimontii and A. baylyi/genomic species 11 have similarities of 99%. The other species have less than 95% similarity with each other.

b. Identification of the Different Species of Acinetobacter Based on the Partial Sequences of the rpoB Gene

The SVARAP programme enabled identification of 2 variable regions bounded by conserved regions, allowing the generation of universal primers:

-   -   region 1: between positions 2900 and 3250, and     -   region 2: between positions 3250 and 3700 bp (FIG. 1).

These regions were amplified using primers from all species of Acinetobacter and all strains of A. baumannii. The size of region 1 is 350 bp and region 2 has 450 bp. The similarity percentage between the different species of region 1 varies from 78.6 to 95.4% for all species except 2 pairs. As for the complete sequence, A. baylyi/genomic species 11 and A. junii/A. grimontii have the highest similarity values, respectively 98 and 99.1%, whereas the other species have less than 96%. The similarity percentage for region 2 is between 75.8 and 95.3% for all species, again with the exception of species A. junii/A. grimontii and A. baylyi/genospecies 11 which have the highest similarities i.e. 98.8 et 99.6% respectively, whereas the other species have less than 96% similarity between each other.

The intra-specific similarity of the different strains of A. baumannii for region 1 varies from 98.3 to 100% with the exception of strain CIP 103655. This latter strain only has between 94.9 and 95.7% similarity with the other strains. In the same manner, region 2 varies from 98.7 to 100% for all strains of A. Baumanii with the exception of strain CIP 103655. This strain has similarities of between 93.6 and 94.4% with the other strains of the species. The closest species to A. baumannii are genomic species 3 for region 1 and A. calcoaceticus for region 2, with similarities of 95.1% and 93.6% respectively. These are much lower values than for intraspecific variability with the exception of strain CIP 103655 for which the most distant strain of A. baumannii has 94.9% and 93.6% similarity in regions 1 and 2 respectively.

Overall, sequence variability ranges from 0.4 to 24.2% for the partial sequences, compared with 0.8 to 16.9% for complete rpoB sequences. The 2 partial sequences therefore allow non-ambiguous identification of the 24 species.

c. Analysis of the Regions Flanking the rpoB Gene (Intergenic Spacer rplL-rpoB and Intergenic Spacer rpoB-rpoC)

The size of the 2 intergenic spacers varies according to species. The size of the spacer between rplL and rpoB varies from 301 to 310 bp (Table 1). Between species, the similarity rate of this rp/L-rpoB spacer varies from 80.8 to 96.9%, except that the intergenic spacer is identical between A. junnii and A. grimontii, and the pairs of species such as A. baylyi-genomic species 11 and A. lwoffii-genomic species 9 have similarity rates of between 98.4 and 99.7%.

The size of the intergenic spacer between rpoB and rpoC varies from 86 to 177 bp (Table 1) with similarity rates between species of between 70.2 and 96.5%, except for A. junnii/A. grimontii which have a high similarity of 99.5%, and within the Acb complex (A. calcoaceticus, A. baumannii and genomic species 3) whose similarity rates lie between 98.5 and 99.0% for the intergenic spacer rpoB-rpoC. On the other hand, compared with the spacer rplL-rpoB, A. baylyi-genomic species 11 and A. lwoffii-genomic species 9 only have 83.8 and 87.9% similarity respectively for the rpoB-rpoC intergenic spacer.

Within the A. baumannii species, the size of the rplL-rpoB intergenic spacer is 305 bp for all strains, with the exception of strain CIP 103655 for which the size is 304 bp. The rpoB-rpoC intergenic spacer has a size of 86 bp for all strains. Again in this species, the similarity rate in the rpolL-rpoB spacer varies from 99 to 100% for all strains with the exception of strain CIP 103655. This latter strain has between 96.1 and 96.4% similarity with the other strains. The other intergenic spacer rpoB-rpoC has 100% similarity for all strains with the exception of strain CIP 103655 for which it has 97.7 to 98.8% similarity with the other strains. The closest species to A. baumannii is genomic species 3 for the rplL-rpoB spacer and A. calcoaceticus for the rpoB-rpoC spacer, with respective similarities of 95.9% and 98.5%. These are much higher values than intra-specific similarity, with the exception of strain CIP 103655 for which species of A. baumannii have similarities of 96.1% and 97.7% respectively for intergenic spacers rplL-rpoB and rpoB-rpoC.

As arises from the positions of the primers of sequences SEQ. ID. no 5, 6, 7 and 8, the fragments corresponding to the amplicons obtained using these primers have sequences which overspan those of the actual intergenic spacers at the 5′ and 3′ ends, but sequences SEQ. ID. no 121 to 144 and 165 to 188 given in the sequence listing appended to this description correspond to the complete intergenic spacers and do not overspan genes rp/L, rpoB and rpoC respectively.

d. Phylogenetic Analysis of Acinetobacter Species

The phylogenetic tree constructed with the complete sequences of the rpoB gene and constructed using the neighbour-joining technique, is supported by very high bootstrap values (FIG. 2). The number of bootstrap values ≧75% is 17/22 when using the complete rpoB gene, whereas it is only 7/22 when using the 16S rRNA gene (p<0.01). All the species are well separated into different groups. The tree based on the partial rpoB gene (concatenated region 1 and region 2) shows a homogeneous group of A. baumannii strains. Strain CIP 103655 appears in the same group but is clearly separate from the other isolates of A. baumannii. This grouping is supported by a bootstrap value of 85%.

2.4—Discussion

With the exception of the 16S rRNA gene, there currently does not exist any sequencing of house-keeping genes on all species of Acinetobacter. The sequences of genes gyrB and recA are not available for the 10 species most recently described. Yamamoto et al (1996, 1999) and Krawczyk et al (2002) have sequenced the gyrB and recA genes of 14 species and compared this technique with DNA-DNA hybridisation (Bouvet and Jeanjean, 1989; Bouvet and Grimont, 1986; Tjernberg and Ursing, 1989). By constructing a tree based on the rpoB gene which incorporates 14 species, no congruency is observed between the different species. However, the tree based on the rpoB gene has significantly more bootstrap values of ≧75% (11/12) than the tree based on the 16S rRNA gene (4/12), gyrB (5/12) and recA (6/12) (p<0.01, p=0.01 and p=0.02 respectively) (FIG. 4). This demonstrates the robustness of the tree based on the rpoB gene. A. lwoffi and Acinetobacter genomic species 9 are 100% identical on the gyrB gene, but are separated on the sequence of gyrD and recA (Yamamoto et al., 1999; Krawczyk et al (2002). The species that are ill-delimited by the rpoB gene are the pairs A. grimontii/A. junii and A. baylii/genospecies 9. Unfortunately, it is impossible to compare them at gyrB and recA, the sequences of A. grimontii and A. baylii not being available.

For the routine molecular identification of Acinetobacter bacteria, each of the partial sequences of the rpoB gene and of its 2 boundary intergenic spacers can be used on account of its discriminatory power and length. The disadvantage of using only one of these sequences is the lack of good discrimination between the pairs A. grimontii/A. junii and A. baylii/genomic species 9 (Tables 4 to 11). However, this disadvantage can be reduced by combining the sequence of at least 2 of these hypervariable sequences. Owing to its size we believe it is preferable to start with the sequence of region 1 since it can be used for perfect identification of 20 species out of 24. If the sequences obtained are those of A. grimontii/A. junii, it is better to subsequently to carry out the sequence of region 2 which better differentiates between these 2 species. If the sequence obtained is closer to A. baylii/genospecies 9, it is preferable to determine the sequence of the rpoB-rpoC spacer which discriminates better between these 2 species.

The intra-specific variability of the short fragments observed in the A. baumannii species shows that, with the exception of strain CIP 103655, all the isolates have distinctly lower similarities than those observed between A. baumannii and the species closest to it. However the low similarities observed between the A. baumannii strain CIP 103655 and the other isolates of the species show that the identification of some isolates of this species may remain ambiguous. The A. baumannii species is the most frequent species affecting man. The results show that the CIP 103655 strain is different to the 24 categorized species and is probably not a strain of the A. baumannii species.

To conclude, the results obtained through the use of partial sequences of the rpoB gene and the intergenic spacers rplL-rpoB and rpoB-rpoC show that these tools are efficient for the routine molecular identification of Acinetobacter strains. However, owing to the strong similarity between some species, additional work to examine intra-specific similarities in several species will be necessary. Also, the status of some strains such as strain A. baumannii CIP 103655 and of some species such as A. grimontii and A. baylii, must be investigated by DNA-DNA hybridisation and sequences of other house-keeping genes (recA and gyrB).

TABLE 1 Acinetobacter strains investigated. SEQ. ID. SEQ. ID SEQ. ID. complete intergenic spacers rpoB- rpoB- rpoB- rp/L-rpoB rpoB-rpoC Species Strain complete region 1 region 2 SEQ. ID. n^(o) Size SEQ. ID. Size genomic species 1, CIP 81.8^(T) 9 33 77 121 305 165 86 A. calcoaceticus genomic species 2, CIP 70.34^(T) 10 34 78 122 305 166 86 baumannii 1072.1 (ref) 57 101 144 305 189 86 CIP 53.77 58 102 145 305 190 86 CIP 53.79 59 103 146 305 191 86 CIP 54.97 60 104 147 305 192 86 CIP 54.147 61 105 148 305 193 86 CIP 64.1 62 106 149 305 194 86 CIP 68.38 63 107 150 305 195 86 CIP 70.8 64 108 151 305 196 86 CIP 70.9 65 109 152 305 197 86 CIP 70.10 66 110 153 305 198 86 CIP 70.21 67 111 154 305 199 86 CIP 70.22 68 112 155 305 200 86 CIP 70.24 69 113 156 305 201 86 CIP 70.28 70 114 157 305 202 86 CIP 70.32 71 115 158 305 203 86 CIP 70.33 72 116 159 305 204 86 CIP 70.35 73 117 160 305 205 86 CIP 103572 74 118 161 305 206 86 CIP 103655 75 119 162 304 207 86 CIP 105742 76 120 163 304 208 86 genomic species 3 CIP 70.15 11 35 79 123 305 167 86 genomic species 4, CIP 64.3^(T) 12 36 80 124 308 168 172 A. haemolyticus genomic species 5, CIP 64.5^(T) 13 37 81 125 308 169 149 A. junii genomic species 6 CIP A165 14 38 82 126 308 170 170 genomic species 7, CIP 64.6^(T) 15 39 83 127 301 171 141 A. johnsonii genomic species 8, CIP 64.10^(T) 16 40 84 128 308 172 177 A. lwoffii genomic species 9 CIP 64.7 17 41 85 129 306 173 150 genomic species 10 CIP 70.12 18 42 86 130 307 174 144 genomic species 11 CIP 63.46 19 43 87 131 304 175 154 genomic species 12, CIP 103788^(T) 20 44 88 132 304 176 89 A. radioresistens genomic species 13 CIP 70.18 21 45 89 133 309 177 154 genomic species 16 CIP 64.2 22 46 90 134 309 178 153 A. schindleri CIP 107287^(T) 23 47 91 135 310 179 159 A. ursingii CIP 107286^(T) 24 48 92 136 308 180 136 A. baylyi CIP 107474^(T) 25 49 93 137 304 181 88 A. bouvetii CIP 107468^(T) 26 50 94 138 305 182 156 A. gerneri CIP 107464^(T) 27 51 95 139 309 183 170 A. grimontii CIP 107470^(T) 28 52 96 140 308 184 150 A. tandoii CIP 107469^(T) 29 53 97 141 306 185 156 A. tjernbergiae CIP 107465^(T) 30 54 98 142 307 186 143 A. towneri CIP 107472^(T) 31 55 99 143 307 187 157 A. parvus CIP 108168^(T) 32 56 100 144 308 188 143

TABLE 2 Primers used to amplify, the rpoB gene and its flanking regions SEQ Tm ID No. Primer Sequence (5′-3′) Position (° C.) NO:  1. AcintF^(a) GGTAAAGTDACRCCTAAAGGT 60° C. 209  2. AcintR^(a) GTATGAACGTGGGDCAGATT 58° C. 210  3. Ac28F^(a) GTDGGTACVGGYATGGAA 52° C. 211  4. Ac1754R^(a) GAACGYGCRTGCATYTTGTCA 60° C. 212  5. Ac822F CGYAAAGAYTTGAAAGAAGA 54° C. 213  6. Ac840R CTTCTTTCAARTCTTTRCGRT 60° C. 214  7. Ac660F GAYGTDAAAGAYTCATCTTTA 54° C. 215  8. Ac1720R GAACGYGCRTGCATYTTGT 60° C. 216  9. Ac660R CGTAAAGATGARTCTTTHAC 54° C. 217 10. Ac1700F GACAARATGCAYGCRCGTT 60° C. 218 11. Ac696F* TAYCGYAAAGAYTTGAAAGAAG 60° C. 1 12. Ac1093R* CMACACCYTTGTTMCCRTGA 60° C. 2 13. Ac1055F* GTGATAARATGGCBGGTCGT 60° C. 3 14. Ac1598R* CGBGCRTGCATYTTGTCRT 58° C. 4 15. Acint1F^(b) AAGAAGCWGGYGCTAMAG − 55° C. 219 16. Acint2F^(b) CTKGGYCTKAAAGAAGCYAA − 58° C. 220 17. Acint3F^(b) CTGCTGCYGYTGTTGAAGA − 58° C. 221 18. Acint1R^(b) GGTAGTTRATGGTTTCMGG + 56° C. 222 19. Acint2R^(b) GTTRATGGTTTCMGGCTTYTT + 59° C. 223 20. Acint3R^(b) GGTTTCMGGCTTYTTAACTT + 56° C. 224 21. Ac1F^(a) ATGGCWTACTCAYATACYGA 1 57° C. 225 22. Ac4F^(a) GCWTACTCATAYACYGARAA 4 56° C. 226 23. Ac8F^(a) ACTCATAYACYGARAARAAAC 8 56° C. 227 24. Ac361F GARCAAGAAGTMTACATGGG 361 58° C. 228 25. Ac1215F GTTCAACCGYCGTWTSGGT 1215 59° C. 229 26. Ac1503F GATCAACGCCAAGCCDGT 1503 57° C. 230 27. Ac2071F GGYTCRAACATGCAGCGT 2071 56° C. 231 28. Ac2267F GYGTVGAYATCTACAACCT 2267 55° C. 232 29. Ac3684F TGAYGGHCGTACDGGYG 3684 56° C. 233 30. Ac3753F CCAYTTRGTDGAYGACAAAAT 3753 56° C. 234 31. Ac3850F TTCGGTGGTCAGCGYTTC 3850 57° C. 235 32. Ac28R GTTTYTTYTCRGTRTATGAGT 28 56° C. 236 33. Ac55R GCAAYTTRCYAAARTYCTT 55 59° C. 237 34. Ac211R CAGCATTGCCRGARTARCT 211 57° C. 238 35. Ac380R CCCATGTAKACTTCTTGYTC 380 58° C. 239 36. Ac1221R GTTGAACTTCATVCGDCCWA 1221 55° C. 240 37. Ac1523R GCHACHGGCTTGGCGTT 1523 56° C. 241 38. Ac2093R GCCTGACGCTGCATGTT 2093 55° C. 242 39. Ac2314R^(a) TGTTCTGGTTBGAACGVGT 2314 56° C. 243 40. Ac2928R^(a) GHGCHGCTTCTTCRAAGA 2928 55° C. 244 41. Ac2936R^(a) CGYTCACGHGCHGCTTCT 2936 55° C. 245 42. Ac1170F GCTTCCATYTGGCGHACRT 1170 58° C. 246 43. Ac1705F GTACGTCACGBACYTCRAA 1705 58° C. 247 44. Ac1804F TCCATRAACTGDGAYAAYTG 1804 56° C. 248 45. Ac2231F GTATCACGYGCDACACAHGA 2231 60° C. 249 46. Ac2348F GTCATGAAYGCDACRCGCA 2348 58° C. 250 47. Ac1379R CGGTTACCYAARTGRTCRAT 1379 58° C. 251 48. Ac1391R GAACGNACRCGVCGGTTA 1391 58° C. 252 49. Ac2325R GTTRATACADGTRTTYTGGTT 2325 56° C. 253 50. Ac2439R GAACGCRACRCGCATGTT 2439 56° C. 254 51. Ac2442R CATGAACGCRACRCGCAT 2442 56° C. 255

TABLE 3 Primers used to amplify and sequence region 1 and region 2 of the rpoB gene and its boundary spacers in the Acineto- bacter species subject of the present study. SEQ. ID. Tm Primers n^(o) Sequence (5′-3′) Position* (° C.) Target Ac696F 1 TAYCGYAAAGAYTTGAAAGAAG +2916 60° C. rpoB region 1 Ac1093R 2 CMACACCYTTGTTMCCRTGA +3267 60° C. rpoB region 1 Ac1055F 3 GTGATAARATGGCBGGTCGT +3263 60° C. rpoB region 2 Ac1598R 4 CGBGCRTGCATYTTGTCRT +3773 58° C. rpoB region 2 AcintLBF 5 GAAGARCTTAAGAMDAARCTTG −361 60° C. Spacer rp/L-rpoB AcintLBR 6 CGTTTCTTTTCGGTATATGAGT +29 60° C. Spacer rp/L-rpoB AcintBCF 7 GTTCTTTAGGTATCAACATTGAA +4048 60° C. Spacer rpoB-rpoC AcintBCR 8 GACGCAAGACCAATACGRAT +4207 59° C. Spacer rpoB-rpoC *i.e. the position of the first nucleotide of the primer sequence relative to the rpoB gene.

TABLE 4 Comparison of similarity rates (%) of the rpoB gene (4089 bp) between the different Acinetobacter species 1 2 3 4 5 6 7 8 9 10 11 12  [1] A. calcoaceticus  [2] A. genospecies 3 93.9  [3] A. baumannii 92.0 93.8  [4] A. genospecies 16 88.6 88.7 89.4  [5] A. parvus 87.9 88.3 89.0 93.9  [6] A. genospecies 13 89.4 89.5 90.0 94.4 93.7  [7] A. tjernbergiae 89.4 89.0 89.4 91.9 91.6 93.3  [8] A. grimonti 87.7 87.9 88.6 91.8 91.7 92.1 90.1  [9] A. junii 87.5 87.8 88.6 91.6 91.8 92.0 90.0 99.2 [10] A. haemolyticus 88.0 88.3 89.1 92.5 91.8 92.1 90.4 91.7 91.9 [11] A. genospecies 6 87.8 87.8 87.5 90.1 89.5 90.4 89.8 90.1 90.1 90.6 [12] A. bouvetii 84.8 85.2 85.6 85.8 85.4 86.1 85.4 84.3 84.4 85.3 84.8 [13] A. johnsonii 86.6 86.8 87.2 87.8 87.7 88.4 87.6 86.8 86.7 87.3 86.6 88.6 [14] A. genospecies 9 85.5 86.3 86.2 86.5 86.1 86.2 85.2 85.1 85.0 85.9 85.1 87.6 [15] A. lwoffi 85.7 86.4 85.9 86.8 85.9 86.9 85.7 85.2 85.0 86.1 85.4 86.9 [16] A. schindleri 86.0 86.7 86.9 87.2 86.8 87.4 86.4 85.9 85.7 86.3 85.7 88.4 [17] A. towneri 85.1 85.2 85.7 86.2 86.0 86.5 85.5 86.4 86.5 86.5 86.0 86.0 [18] A. tandoii 86.4 87.0 86.7 87.5 87.4 88.0 87.2 87.3 87.4 87.9 87.1 86.4 [19] A. baylyi 86.5 86.6 87.2 87.4 86.7 87.6 86.6 86.6 86.7 87.2 86.3 86.2 [20] A. genospecies 11 86.6 86.9 87.3 87.6 87.0 87.9 86.9 86.8 86.9 87.4 86.5 86.3 [21] A. genospecies 10 86.6 86.9 87.3 87.4 87.7 88.2 87.6 87.2 87.2 87.5 86.9 86.4 [22] A. gerneri 86.5 86.7 87.6 86.9 86.9 87.7 87.4 87.3 87.3 87.5 86.9 86.8 [23] A. ursingii 85.7 86.0 85.6 85.4 85.7 85.9 86.3 85.3 85.3 86.2 86.5 84.3 [24] A. radioresistense 84.2 84.5 84.9 84.6 84.4 84.4 84.1 84.4 84.2 84.4 84.2 83.1 13 14 15 16 17 18 19 20 21 22 23  [1] A. calcoaceticus  [2] A. genospecies 3  [3] A. baumannii  [4] A. genospecies 16  [5] A. parvus  [6] A. genospecies 13  [7] A. tjernbergiae  [8] A. grimonti  [9] A. junii [10] A. haemolyticus [11] A. genospecies 6 [12] A. bouvetii [13] A. johnsonii [14] A. genospecies 9 88.4 [15] A. lwoffi 88.4 93.3 [16] A. schindleri 88.7 90.7 90.5 [17] A. towneri 88.0 87.3 86.7 87.0 [18] A. tandoii 87.9 86.4 86.8 87.4 87.1 [19] A. baylyi 87.0 86.9 86.9 86.7 86.0 86.7 [20] A. genospecies 11 87.3 87.1 87.2 86.9 86.1 86.8 99.2 [21] A. genospecies 10 87.4 86.6 86.7 87.4 85.5 87.4 92.3 92.5 [22] A. gerneri 87.7 86.3 86.4 86.7 87.0 87.6 88.7 88.9 89.0 [23] A. ursingii 85.5 85.1 84.9 85.2 85.3 86.5 85.3 85.5 85.3 86.1 [24] A. radioresistense 83.2 84.6 84.3 84.9 84.6 83.9 84.1 84.0 83.7 84.3 85.2

TABLE 5 Comparison of similarity rates (%) of sequences (301-310 bp) of the rp/L-rpoB spacer in the different Acinetobacter species. 1 2 3 4 5 6 7 8 9 10 11 12  [1] A. calcoaceticus  [2] genospecies 3 92.8  [3] A. baumannii 90.6 95.9  [4] genospecies 13 84.0 86.8 86.5  [5] genospecies 16 86.5 87.4 86.8 93.4  [6] A. parvus 83.0 86.2 86.5 96.9 93.4  [7] A. tjernbergiae 85.5 87.1 86.5 95.0 93.7 94.0  [8] A. junii 87.7 88.4 88.4 91.5 93.4 91.2 93.1  [9] A. grimontii 87.7 88.4 88.4 91.5 93.4 91.2 93.1 100.0 [10] A. haemolyticus 85.8 87.1 86.5 93.4 93.7 92.1 93.1 93.4 93.4 [11] genospecies 6 87.1 87.4 86.2 91.2 93.1 90.6 92.1 93.1 93.1 91.2 [12] genospecies 9 87.7 86.8 86.8 84.0 85.8 83.0 85.2 86.5 86.5 85.5 85.8 [13] A. lwoffii 86.8 86.5 86.5 83.0 84.6 82.7 85.2 85.5 85.5 84.6 85.5 98.4 [14] A. schindleri 87.4 87.7 88.1 83.6 85.5 83.6 85.8 87.4 87.4 85.5 85.8 96.2 [15] A. bouvetii 87.7 86.5 86.5 84.6 85.2 84.3 86.2 86.5 86.5 86.2 85.5 91.8 [16] A. johnsonii 84.3 84.6 84.9 81.1 82.4 80.8 82.7 82.1 82.1 82.4 82.1 88.1 [17] A. towneri 84.9 85.8 87.1 87.1 85.5 86.5 87.4 84.6 84.6 85.8 84.9 89.0 [18] A. tandoii 86.2 85.8 85.8 84.0 84.3 83.6 85.2 84.9 84.9 84.3 84.3 89.0 [19] A. baylyi 82.7 82.4 83.0 81.4 83.6 82.4 82.7 83.6 83.6 81.8 82.7 86.2 [20] genospecies 11 83.0 82.7 83.3 81.8 84.0 82.7 83.0 84.0 84.0 82.1 82.7 86.5 [21] genospecies 10 84.9 84.6 84.9 84.3 85.5 84.9 85.5 86.2 86.2 83.6 84.9 88.1 [22] A. gerneri 86.8 85.5 85.8 83.0 84.6 83.6 84.9 85.2 85.2 83.6 84.0 88.4 [23] A. radioresistense 86.2 87.1 88.4 86.8 87.4 86.2 86.8 87.7 87.7 86.8 85.2 86.8 [24] A. ursingii 85.8 84.9 85.5 85.2 86.5 84.9 86.8 85.5 85.5 84.9 85.2 85.5 13 14 15 16 17 18 19 20 21 22 23  [1] A. calcoaceticus  [2] genospecies 3  [3] A. baumannii  [4] genospecies 13  [5] genospecies 16  [6] A. parvus  [7] A. tjernbergiae  [8] A. junii  [9] A. grimontii [10] A. haemolyticus [11] genospecies 6 [12] genospecies 9 [13] A. lwoffii [14] A. schindleri 95.9 [15] A. bouvetii 91.2 91.5 [16] A. johnsonii 87.7 87.4 86.5 [17] A. towneri 88.4 89.3 91.2 87.4 [18] A. tandoii 88.4 89.3 93.1 84.9 90.3 [19] A. baylyi 85.2 85.8 85.5 89.3 87.1 84.9 [20] genospecies 11 85.5 86.2 85.8 89.6 87.4 85.2 99.7 [21] genospecies 10 87.1 87.7 90.3 86.8 89.3 89.6 92.5 92.8 [22] A. gerneri 88.4 87.7 88.7 85.5 88.4 88.1 91.5 91.8 92.8 [23] A. radioresistense 86.2 85.8 86.2 84.9 86.5 84.9 83.0 83.3 86.5 86.5 [24] A. ursingii 85.5 84.9 87.7 85.5 85.8 86.2 85.2 85.5 86.8 87.7 90.3

TABLE 6 Similarity rates (%) of sequences (301-310 bp) of the rpoB-rpoC spacer (86-177 bp) in the different Acinetobacter species. 1 2 3 4 5 6 7 8 9 10 11 12  [1] genospecies 6  [2] A. haemolyticus 92.4  [3] A. junii 90.4 89.4  [4] A. grimontii 90.9 89.9 99.5  [5] A. calcoaceticus 90.4 89.9 91.4 91.4  [6] genospecies 3 90.9 89.9 91.9 91.9 99.0  [7] A. baumannii 90.4 89.9 91.4 91.4 98.5 98.5  [8] genospecies 13 76.3 75.3 78.8 79.3 92.9 93.4 92.9  [9] genospecies 16 75.3 75.3 77.8 78.3 91.9 92.4 91.9 96.5 [10] A. parvus 79.3 79.3 79.8 80.3 91.4 91.4 91.4 86.4 85.9 [11] A. tjernbergiae 80.3 80.8 81.3 81.8 93.4 93.4 93.4 86.4 86.9 91.4 [12] A. tandoii 74.2 77.8 75.8 76.3 90.4 91.4 90.4 79.8 80.3 77.3 79.8 [13] A. towneri 74.2 77.3 78.8 79.3 88.4 89.4 88.9 76.8 76.8 76.3 78.8 85.4 [14] A. baylyi 82.8 81.8 80.3 80.8 88.4 87.9 87.9 84.8 86.4 87.4 87.4 85.9 [15] genospecies 11 78.3 79.8 77.3 77.8 88.9 89.9 89.4 77.3 77.8 79.3 81.3 84.3 [16] genospecies 10 75.3 77.3 77.3 76.8 88.4 88.4 88.9 79.3 79.8 81.8 84.8 72.7 [17] A. gerneri 78.3 78.8 80.3 80.8 89.4 90.4 89.4 74.7 75.3 74.2 75.3 76.8 [18] A. bouvetii 70.7 73.7 74.7 75.3 89.9 90.9 89.9 89.4 91.4 84.3 85.4 81.8 [19] A. schindleri 70.2 73.7 72.7 73.2 90.9 91.9 90.9 88.9 90.4 84.3 85.9 80.8 [20] A. johnsonii 75.3 77.8 74.2 73.7 89.4 89.4 89.4 73.2 73.7 75.8 76.8 76.3 [21] genospecies 9 76.8 79.8 80.8 81.3 90.4 91.4 90.4 80.3 82.3 79.3 81.3 81.8 [22] A. lwoffii 74.7 77.3 78.8 79.3 90.4 91.4 90.4 82.3 83.8 81.3 82.8 83.8 [23] A. radioresistense 86.4 86.4 85.4 85.4 94.9 94.9 94.9 88.4 87.9 91.9 93.4 87.9 [24] A. ursingii 77.3 75.3 79.8 79.3 90.9 91.4 91.9 81.3 82.8 85.4 88.4 77.8 13 14 15 16 17 18 19 20 21 22 23  [1] genospecies 6  [2] A. haemolyticus  [3] A. junii  [4] A. grimontii  [5] A. calcoaceticus  [6] genospecies 3  [7] A. baumannii  [8] genospecies 13  [9] genospecies 16 [10] A. parvus [11] A. tjernbergiae [12] A. tandoii [13] A. towneri [14] A. baylyi 82.8 [15] genospecies 11 84.3 83.8 [16] genospecies 10 75.3 82.8 80.8 [17] A. gerneri 71.7 82.3 70.7 74.7 [18] A. bouvetii 79.8 83.3 75.3 76.3 74.2 [19] A. schindleri 78.3 84.3 75.3 77.8 71.7 92.9 [20] A. johnsonii 74.2 81.8 72.2 75.8 77.3 76.3 77.8 [21] genospecies 9 82.8 82.3 78.8 77.3 76.3 84.8 84.8 80.8 [22] A. lwoffii 82.3 85.9 78.3 76.8 74.2 83.8 81.8 73.2 87.9 [23] A. radioresistense 86.4 90.9 85.9 89.9 84.3 86.9 85.4 86.4 86.9 87.4 [24] A. ursingii 77.8 85.4 79.3 81.3 72.2 77.8 77.8 76.8 77.8 78.3 88.4

TABLE 7 Comparison of similarity rates (%) of sequences (350 bp) of the partial sequences of rpoB region 2 in the different Acinetobacter species. 1 2 3 4 5 6 7 8 9 10 11 12  [1] A. baumannii  [2] genospecies 3 95.1  [3] A. calcoaceticus 88.3 90.6  [4] A. grimonti 87.1 86.6 88.0  [5] A. junii 86.9 86.3 87.1 99.1  [6] genospecies 16 86.0 84.3 84.6 90.3 89.4  [7] A. parvus 87.1 85.7 84.0 91.4 90.6 95.4  [8] genospecies 13 87.4 86.9 85.7 90.6 89.7 93.4 93.1  [9] A. johnsonii 85.1 84.3 84.6 90.0 89.4 89.4 91.1 91.7 [10] A. tjernbergiae 87.1 86.3 85.4 90.6 89.7 92.3 92.9 93.1 93.1 [11] genospecies 6 83.7 82.9 82.9 87.4 87.1 89.4 88.3 87.1 87.7 87.7 [12] A. haemolyticus 87.7 85.4 85.1 87.7 87.4 92.0 89.7 91.1 89.1 90.0 90.3 [13] A. schindleri 84.6 84.0 82.9 89.1 88.6 87.7 88.0 88.3 86.0 87.1 85.4 86.3 [14] A. baylyi 85.1 84.0 82.6 85.1 84.9 86.0 85.4 84.6 86.0 85.1 85.7 85.7 [15] genospecies 11 85.1 84.3 82.9 85.1 84.9 85.7 85.1 84.9 85.7 85.4 85.7 85.7 [16] A. bouvetii 84.6 84.6 81.1 85.4 85.7 84.9 85.4 85.4 86.0 84.9 83.7 84.9 [17] genospecies 10 82.9 82.6 80.6 84.6 83.7 84.9 84.9 85.1 84.3 84.9 82.6 84.9 [18] A. gerneri 84.9 85.7 82.3 89.1 88.9 85.4 86.9 85.7 87.4 86.9 85.4 85.1 [19] genospecies 9 85.4 84.3 82.3 83.7 84.0 86.0 85.1 85.7 86.0 84.9 84.6 86.0 [20] A. lwoffii 83.7 85.1 83.1 83.4 83.7 85.7 84.6 87.1 85.1 84.6 84.0 85.7 [21] A. towneri 81.7 80.9 81.4 85.1 85.4 84.9 84.0 83.7 87.1 83.4 83.4 84.0 [22] A. ursingii 82.6 82.0 82.0 84.9 84.6 82.9 84.0 83.7 83.7 85.1 84.6 82.9 [23] A. tandoii 83.4 82.6 82.0 88.6 88.3 89.4 90.0 86.9 88.0 88.3 86.9 88.0 [24] A. radioresistense 79.7 78.9 78.6 82.0 81.1 82.0 82.0 80.0 79.4 81.7 80.6 79.4 13 14 15 16 17 18 19 20 21 22 23  [1] A. baumannii  [2] genospecies 3  [3] A. calcoaceticus  [4] A. grimonti  [5] A. junii  [6] genospecies 16  [7] A. parvus  [8] genospecies 13  [9] A. johnsonii [10] A. tjernbergiae [11] genospecies 6 [12] A. haemolyticus [13] A. schindleri [14] A. baylyi 84.9 [15] genospecies 11 85.7 98.0 [16] A. bouvetii 86.3 90.0 89.4 [17] genospecies 10 85.1 88.6 88.0 85.1 [18] A. gerneri 85.7 87.1 87.1 89.1 86.0 [19] genospecies 9 86.9 86.0 86.9 86.3 85.1 86.6 [20] A. lwoffii 86.0 85.4 86.6 85.4 84.3 86.3 93.7 [21] A. towneri 82.0 83.7 83.1 83.4 80.9 86.3 86.3 84.0 [22] A. ursingii 83.4 82.0 82.6 84.0 81.7 85.4 80.6 81.7 82.0 [23] A. tandoii 85.7 83.4 83.7 85.4 82.3 87.4 85.1 85.7 84.9 83.7 [24] A. radioresistense 82.0 78.6 79.4 80.3 79.7 83.1 80.0 80.0 78.6 80.0 83.4

TABLE 8 Comparison of similarity rates (%) of sequences (450 bp) of the partial sequences of rpoB region 2 in the different Acinetobacter species. 1 2 3 4 5 6 7 8 9 10 11 12  [1] A. calcoaceticus  [2] genospecies 3 94.2  [3] A. baumannii 93.6 91.8  [4] genospecies 13 89.3 90.0 88.4  [5] A. tjernbergiae 90.0 90.7 89.1 93.8  [6] genospecies 16 88.2 88.7 89.1 93.3 93.1  [7] A. parvus 88.4 88.7 89.6 93.6 93.1 94.9  [8] A. baylyi 84.7 84.9 84.4 86.9 85.6 86.2 86.2  [9] genospecies 11 84.2 84.9 84.4 86.4 85.6 86.2 86.2 99.6 [10] genospecies 10 84.0 84.2 84.9 84.4 83.8 87.3 86.9 94.9 95.3 [11] A. bouvetii 86.2 85.8 85.1 83.8 86.0 85.6 84.9 87.3 87.3 88.0 [12] A. schindleri 82.9 85.1 84.2 83.6 83.3 85.3 84.7 87.1 87.1 87.3 90.9 [13] A. johnsonii 84.7 85.3 85.8 85.8 86.0 86.7 86.2 87.1 87.1 86.4 89.8 88.7 [14] genospecies 9 83.6 85.1 83.8 83.6 83.8 85.1 86.0 86.0 86.0 85.8 86.4 88.0 [15] A. lwoffii 83.6 85.6 83.3 84.4 84.0 85.8 84.2 86.4 86.4 85.8 86.4 88.0 [16] A. gerneri 81.8 80.0 82.0 81.6 80.9 82.4 81.6 87.3 87.3 86.7 84.0 83.3 [17] A. tandoii 82.2 82.7 83.1 83.3 83.3 83.1 83.1 82.9 82.9 82.2 83.1 81.8 [18] A. towneri 83.6 83.6 83.6 83.1 82.4 82.9 83.3 83.3 83.3 83.8 84.0 84.9 [19] A. haemolyticus 83.3 83.1 84.4 81.3 82.4 82.7 82.0 84.7 84.7 83.8 81.8 81.8 [20] genospecies 6 82.0 82.0 82.0 82.0 82.0 83.8 82.2 81.8 81.8 81.8 81.3 80.7 [21] A. ursingii 81.8 81.3 80.7 81.6 82.2 79.6 79.8 80.0 79.6 78.2 79.1 81.1 [22] A. grimonti 80.9 81.6 81.6 82.2 82.2 83.6 83.1 80.2 80.2 81.6 78.2 80.7 [23] A. junii 80.4 80.9 81.6 81.6 81.1 82.4 82.9 80.4 80.4 81.3 78.4 79.6 [24] A. radioresistense 75.8 76.0 77.1 77.1 76.9 78.0 77.8 78.7 78.2 78.7 77.1 78.2 13 14 15 16 17 18 19 20 21 22 23  [1] A. calcoaceticus  [2] genospecies 3  [3] A. baumannii  [4] genospecies 13  [5] A. tjernbergiae  [6] genospecies 16  [7] A. parvus  [8] A. baylyi  [9] genospecies 11 [10] genospecies 10 [11] A. bouvetii [12] A. schindleri [13] A. johnsonii [14] genospecies 9 86.0 [15] A. lwoffii 86.7 95.1 [16] A. gerneri 83.6 82.2 82.4 [17] A. tandoii 82.4 80.9 80.7 83.1 [18] A. towneri 83.8 85.1 85.1 85.3 88.7 [19] A. haemolyticus 82.4 83.8 82.2 85.1 84.7 86.7 [20] genospecies 6 81.8 81.3 81.8 84.7 83.8 84.7 87.3 [21] A. ursingii 79.8 78.9 79.3 81.1 83.1 84.0 81.6 85.8 [22] A. grimonti 80.9 82.7 83.3 80.9 83.1 84.7 84.9 85.8 81.6 [23] A. junii 80.7 80.9 81.8 81.3 83.6 84.2 85.6 86.0 80.9 98.0 [24] A. radioresistense 76.0 80.7 79.6 80.4 79.1 80.2 80.4 81.8 81.6 83.6 82.4

TABLE 9 Comparison of similarity rates (%) of sequences (350 bp) of the partial sequences of rpoB region 1 in the different A. baumannii strains. Strains 1 2 3 4 5 6 7 8 9 10  [1] 64.1  [2] 70.9 100.0  [3] 70.33 100.0 100.0  [4] 105742 100.0 100.0 100.0  [5] 53.79 100.0 100.0 100.0 100.0  [6] 70.8 99.4 99.4 99.4 99.4 99.4  [7] 54.97 99.4 99.4 99.4 99.4 99.4 100.0  [8] 70.32 98.3 98.3 98.3 98.3 98.3 98.9 98.9  [9] 70.34 98.3 98.3 98.3 98.3 98.3 98.9 98.9 100.0 [10] 68.38 98.3 98.3 98.3 98.3 98.3 98.9 98.9 99.4 99.4 [11] 70.24 98.6 98.6 98.6 98.6 98.6 99.1 99.1 99.7 99.7 99.7 [12] 53.77 99.1 99.1 99.1 99.1 99.1 99.7 99.7 99.1 99.1 99.1 [13] 54.147 99.1 99.1 99.1 99.1 99.1 99.7 99.7 99.1 99.1 99.1 [14] 70.10 99.1 99.1 99.1 99.1 99.1 99.7 99.7 98.6 98.6 98.6 [15] 1072.1 98.9 98.9 98.9 98.9 98.9 99.4 99.4 98.3 98.3 98.3 [16] 70.21 99.1 99.1 99.1 99.1 99.1 99.7 99.7 98.6 98.6 98.6 [17] 70.28 98.9 98.9 98.9 98.9 98.9 99.4 99.4 98.3 98.3 98.3 [18] 70.35 98.9 98.9 98.9 98.9 98.9 99.4 99.4 98.3 98.3 98.3 [19] 70.22 99.1 99.1 99.1 99.1 99.1 99.7 99.7 98.6 98.6 98.6 [20] 103572 98.9 98.9 98.9 98.9 98.9 99.4 99.4 98.3 98.3 98.3 [21] 103655 95.4 95.4 95.4 95.4 95.4 95.4 95.4 94.9 94.9 94.9 Strains 11 12 13 14 15 16 17 18 19 20  [1] 64.1  [2] 70.9  [3] 70.33  [4] 105742  [5] 53.79  [6] 70.8  [7] 54.97  [8] 70.32  [9] 70.34 [10] 68.38 [11] 70.24 [12] 53.77 99.4 [13] 54.147 99.4 100.0 [14] 70.10 98.9 99.4 99.4 [15] 1072.1 98.6 99.1 99.1 99.7 [16] 70.21 98.9 99.4 99.4 100.0 99.7 [17] 70.28 98.6 99.1 99.1 99.7 99.4 99.7 [18] 70.35 98.6 99.1 99.1 99.7 99.4 99.7 100.0 [19] 70.22 98.9 99.4 99.4 99.4 99.1 99.4 99.7 99.7 [20] 103572 98.6 99.1 99.1 99.1 98.9 99.1 99.4 99.4 99.7 [21] 103655 95.1 95.1 95.1 95.1 94.9 95.1 95.4 95.4 95.7 95.4

TABLE 10 Comparison of similarity rates (%) of sequences (450 bp) of the partial sequences of rpoB region 2 in different A. baumannii strains Strains 1 2 3 4 5 6 7 8 9 10  [1] 70.10  [2] 70.21 100.0  [3] 1072.1 99.8 99.8  [4] 103572 99.8 99.8 100.0  [5] 53.77 99.1 99.1 99.3 99.3  [6] 70.22 99.1 99.1 99.3 99.3 99.6  [7] 70.32 99.3 99.3 99.6 99.6 99.3 99.3  [8] 70.34 99.3 99.3 99.6 99.6 99.3 99.3 100.0  [9] 68.38 99.3 99.3 99.6 99.6 99.3 99.3 100.0 100.0 [10] 54.147 99.3 99.3 99.6 99.6 99.3 99.3 100.0 100.0 100.0 [11] 53.79 99.1 99.1 99.3 99.3 99.1 99.6 99.8 99.8 99.8 99.8 [12] 70.9 98.9 98.9 99.1 99.1 98.9 99.3 99.6 99.6 99.6 99.6 [13] 64.1 99.1 99.1 99.3 99.3 99.1 99.6 99.8 99.8 99.8 99.8 [14] 70.33 99.1 99.1 99.3 99.3 99.1 99.6 99.8 99.8 99.8 99.8 [15] 105742 99.1 99.1 99.3 99.3 99.1 99.6 99.8 99.8 99.8 99.8 [16] 54.97 99.1 99.1 99.3 99.3 99.1 99.1 99.8 99.8 99.8 99.8 [17] 70.8 99.1 99.1 99.3 99.3 98.7 98.7 99.3 99.3 99.3 99.3 [18] 70.24 99.6 99.6 99.8 99.8 99.1 99.1 99.8 99.8 99.8 99.8 [19] 70.35 99.6 99.6 99.8 99.8 99.6 99.6 99.8 99.8 99.8 99.8 [20] 70.28 99.6 99.6 99.8 99.8 99.1 99.1 99.3 99.3 99.3 99.3 [21] 103655 94.0 94.0 94.2 94.2 94.2 94.2 93.8 93.8 93.8 93.8 Strains 11 12 13 14 15 16 17 18 19 20  [1] 70.10  [2] 70.21  [3] 1072.1  [4] 103572  [5] 53.77  [6] 70.22  [7] 70.32  [8] 70.34  [9] 68.38 [10] 54.147 [11] 53.79 [12] 70.9 99.8 [13] 64.1 100.0 99.8 [14] 70.33 100.0 99.8 100.0 [15] 105742 100.0 99.8 100.0 100.0 [16] 54.97 99.6 99.3 99.6 99.6 99.6 [17] 70.8 99.1 98.9 99.1 99.1 99.1 99.6 [18] 70.24 99.6 99.3 99.6 99.6 99.6 99.6 99.6 [19] 70.35 99.6 99.3 99.6 99.6 99.6 99.6 99.1 99.6 [20] 70.28 99.1 98.9 99.1 99.1 99.1 99.1 99.1 99.6 99.6 [21] 103655 93.8 93.6 93.8 93.8 93.8 93.6 93.6 94.0 94.0 94.4

TABLE 11 Comparison of similarity rates (%) of the sequences of intergenic spacer rp/L-rpoB in different A. baumannii strains Strains 1 2 3 4 5 6 7 8 9 10  [1] 70.8  [2] 70.33 99.7  [3] 68.38 100.0 99.7  [4] 105742 100.0 99.7 100.0  [5] 64.1 100.0 99.7 100.0 100.0  [6] 103572 100.0 99.7 100.0 100.0 100.0  [7] 54.147 100.0 99.7 100.0 100.0 100.0 100.0  [8] 70.35 100.0 99.7 100.0 100.0 100.0 100.0 100.0  [9] 70.32 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 [10] 70.28 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [11] 70.24 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [12] 70.22 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [13] 70.21 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [14] 70.10 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [15] 54.97 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [16] 53.79 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [17] 53.77 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [18] 70.9 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [19] 70.34 100.0 99.7 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [20] 1072.1 99.3 99.0 99.3 99.3 99.3 99.3 99.3 99.3 99.3 99.3 [21] 103655 96.7 96.4 96.7 96.7 96.7 96.7 96.7 96.7 96.7 96.7 Strains 11 12 13 14 15 16 17 18 19 20  [1] 70.8  [2] 70.33  [3] 68.38  [4] 105742  [5] 64.1  [6] 103572  [7] 54.147  [8] 70.35  [9] 70.32 [10] 70.28 [11] 70.24 [12] 70.22 100.0 [13] 70.21 100.0 100.0 [14] 70.10 100.0 100.0 100.0 [15] 54.97 100.0 100.0 100.0 100.0 [16] 53.79 100.0 100.0 100.0 100.0 100.0 [17] 53.77 100.0 100.0 100.0 100.0 100.0 100.0 [18] 70.9 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [19] 70.34 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [20] 1072.1 99.3 99.3 99.3 99.3 99.3 99.3 99.3 99.3 99.3 [21] 103655 96.7 96.7 96.7 96.7 96.7 96.7 96.7 96.7 96.7 96.4

TABLE 12 Comparison of similarity rates (%) of sequences (301-310 bp) of the intergenic spacer rpoB-rpoC in different A. baumannii strains. Strains 1 2 3 4 5 6 7 8 9 10  [1] 54.97  [2] 103655 98.8  [3] 70.10 100.0 98.8  [4] 70.24 100.0 98.8 100.0  [5] 70.33 100.0 98.8 100.0 100.0  [6] 70.34 100.0 98.8 100.0 100.0 100.0  [7] 70.35 100.0 98.8 100.0 100.0 100.0 100.0  [8] 1072.1 100.0 98.8 100.0 100.0 100.0 100.0 100.0  [9] 103572 100.0 98.8 100 100.0 100.0 100.0 100.0 100.0 [10] 105742 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [11] 70.32 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [12] 70.28 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [13] 70.22 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [14] 70.21 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [15] 70.9 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [16] 70.8 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [17] 68.38 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [18] 64.1 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [19] 54.147 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [20] 53.79 100.0 98.8 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [21] 53.77 98.8 97.7 98.8 98.8 98.8 98.8 98.8 98.8 98.8 98.8 Strains 11 12 13 14 15 16 17 18 19 20  [1] 54.97  [2] 103655  [3] 70.10  [4] 70.24  [5] 70.33  [6] 70.34  [7] 70.35  [8] 1072.1  [9] 103572 [10] 105742 [11] 70.32 [12] 70.28 100.0 [13] 70.22 100.0 100.0 [14] 70.21 100.0 100.0 100.0 [15] 70.9 100.0 100.0 100.0 100.0 [16] 70.8 100.0 100.0 100.0 100.0 100.0 [17] 68.38 100.0 100.0 100.0 100.0 100.0 100.0 [18] 64.1 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [19] 54.147 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [20] 53.79 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 [21] 53.77 98.8 98.8 98.8 98.8 98.8 98.8 98.8 98.8 98.8 98.8

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The invention claimed is:
 1. A mixture of oligonucleotides comprising: (a) an equimolar mixture of each different oligonucleotide defined by a first single sequence consisting of at least 18 consecutive nucleotides of a nucleotide sequence set forth in SEQ ID NOS: 1-5 and 8, where: D represents A, G, or T, Y represents C or T, B represents C, G, or T, R represents A or G, and M represents A or C; or (b) an equimolar mixture of the full-length complementary sequences of the different oligonucleotides set forth in (a).
 2. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO:
 1. 3. A combination of primers comprising: a 5′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 1; and a 3′ primer comprising a mixture of oligonucleotides selected from the group consisting of: (i) an equimolar mixture of each different oligonucleotide defined by a second single sequence consisting of at least 12 consecutive nucleotides of SEQ ID NO:2, where M represents A or C, R represents A or G, and Y represents C or T; and (ii) an equimolar mixture of the full-length complementary sequences of the different oligonucleotides set forth in (i).
 4. A method for determining whether a bacterium belonging to the Acinetobacter genus is present in a sample, the method comprising: (1) contacting the sample with the combination of primers according to claim 3; (2) amplifying the nucleic acids present in the sample by an enzymatic polymerization reaction; and (3) determining the presence of amplification product, wherein the presence of amplification product indicates the presence of a bacterium belonging to the Acinetobacter genus in the sample.
 5. The method according to claim 4, further comprising: (4) determining the presence or absence in the sample of at least one Acinetobacter species selected from the group consisting of A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, by carrying out the following steps comprising: (4a) sequencing the amplification product, and (4b) comparing the sequence of the amplification product obtained in (4a) with at least one sequence selected from the group consisting of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus.
 6. The method according to claim 4, further comprising: (4) determining the presence or absence in the sample of at least one Acinetobacter species selected from the group consisting of A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, by contacting the amplification product with at least one species probe consisting of an rpoB gene fragment, wherein formation of a hybridization complex between the species probe and the amplification product is indicative of the presence in the sample of the Acinetobacter species corresponding to the species probe, and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample.
 7. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising: (1) contacting the sample with the combination of primers according to claim 3 to obtain a first amplification product; and (2) identifying the Acinetobacter species from which the first amplification product was obtained by: sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and if the presence of A. grimontii or A. junii, respectively comprising the rpoB sequences set forth in SEQ ID NO: 28 and SEQ ID NO: 13, is determined, the following steps (3) and (4) are carried out: (3) obtaining a second amplification product by contacting the sample with: a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T; and (4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 77-100; or if the presence of A. baylii or genomic species 11, respectively comprising the rpoB the sequences set forth in SEQ ID NO: 25 and SEQ ID NO: 19 is determined, the following steps (5) and (6) are carried out: (5) obtaining a second amplification product by contacting the sample with: a 5′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and (6) determining whether the second amplification product obtained in (5) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.
 8. The combination of primers according to claim 3, wherein the second single sequence consists of at least 18 consecutive nucleotides of the sequence set forth in SEQ ID NO:
 2. 9. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising: (1) contacting the sample with the combination of primers according to claim 3 to obtain a first amplification product; and (2) identifying the species from which the first amplification product was obtained by: sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and carrying out at least a second amplification wherein the following steps (3) and (4) are carried out: (3) obtaining a second amplification product by contacting the sample with 5′ and 3′ primers selected from the group consisting of: (i) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T; (ii) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 5, or the complementary sequences thereof, where D represents A, G, or T, M represents A or C, and R represents A or G; and a 3′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 6, or the complementary sequence thereof; and (iii) a 5′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and (4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in: SEQ ID NOS: 77-100, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 3 and 4 are selected in (3); SEQ ID NOS: 121-144, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 5 and 6 are selected in (3); or SEQ ID NOS: 165-188, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 7 and 8 are selected in (3).
 10. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising: (1) contacting the sample with the combination of primers according to claim 3 to obtain a first amplification product; and (2) identifying the species from which the first amplification product was obtained by: sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and if the presence of A. baylii or genomic species 11, respectively comprising the rpoB sequences set forth in SEQ ID NO: 25 and SEQ ID NO: 19 is determined, the following steps (3) and (4) are carried out: (3) obtaining a second amplification product by contacting the sample with: a 5′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and (4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.
 11. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising: (1) obtaining a first amplification product by contacting the sample with the combination of primers according to claim 8, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1 and the second single sequence consists of the full-length sequence set forth in SEQ ID NO: 2; and (2) identifying the species from which the first amplification product was obtained by: sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and if the presence of A. grimontii or A. junii, respectively comprising the rpoB the sequences set forth in SEQ ID NO: 28 and SEQ ID NO: 13 is determined, the following steps (3) and (4) are carried out: (3) obtaining a second amplification product by contacting the sample with: a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of the full-length sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T; and (4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 77-100; or if the presence of A. baylii or genomic species 11, respectively comprising the rpoB sequences set forth in SEQ ID NO: 25 or SEQ ID NO: 19 is determined, the following steps (5) and (6) are carried out: (5) obtaining a second amplification product by contacting the sample with: a 5′ primer consisting of the full-length sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and (6) determining whether the second amplification product obtained in (5) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.
 12. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising: (1) obtaining a first amplification product by contacting the sample with the combination of primers according to claim 8, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1 and the second single sequence consists of the full-length sequence set forth in SEQ ID NO:2; and (2) identifying the species from which the first amplification product was obtained by: sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and carrying out at least a second amplification wherein the following steps (3) and (4) are carried out: (3) obtaining a second amplification product by contacting the sample with 5′ and 3′ primers selected from the group consisting of: (i) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of the full-length sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T; (ii) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 5, or the complementary sequences thereof, where D represents A, G, or T, M represents A or C, and R represents A or G; and a 3′ primer consisting of the full-length sequence set forth in SEQ ID NO: 6, or the complementary sequence thereof; and (iii) a 5′ primer consisting of the full-length sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and (4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in: SEQ ID NOS: 77-100, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 3 and 4 are selected in (3); SEQ ID NOS: 121-144, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 5 and 6 are selected in (3); or SEQ ID NOS: 165-188, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 7 and 8 are selected in (3).
 13. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising: (1) obtaining a first amplification product by contacting the sample with the combination of primers according to claim 8, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1 and the second single sequence consists of the full-length sequence set forth in SEQ ID NO:2; and (2) identifying the species from which the first amplification product was obtained by: sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and if the presence of A. baylii or genomic species 11, respectively comprising the rpoB sequences set forth in SEQ ID NO: 28 or SEQ ID NO: 19 is determined, the following steps (3) and (4) are carried out: (3) obtaining a second amplification product by contacting the sample with: a 5′ primer consisting of the full-length sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and (4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.
 14. A combination of primers, comprising: a first pair of primers comprising the combination of primers set forth in claim 8; and a second pair of primers selected from the group consisting of: (i) a 5′ primer comprising an equimolar mixture of each different oligonucleotide defined by a third single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and a 3′ primer comprising an equimolar mixture of each different oligonucleotide defined by a fourth single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T, (ii) a 5′ primer comprising an equimolar mixture of each different oligonucleotide defined by a third single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO:5, or the complementary sequences thereof, where D represents A, G, or T, M represents A or C, and R represents A or G; and a 3′ primer comprising at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 6, or the complementary sequence thereof; and (iii) a 5′ primer comprising at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising an equimolar mixture of each different oligonucleotide defined by a third single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G.
 15. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO:
 2. 16. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO:
 3. 17. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO:
 4. 18. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO:
 5. 19. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO:
 8. 20. A combination of primers comprising: a 5′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3; and a 3′ primer comprising a mixture of oligonucleotides selected from the group consisting of: (i) an equimolar mixture of each different oligonucleotide defined by a second single sequence consisting of at least 12 consecutive nucleotides of SEQ ID NO:4, where: B represents C, G, or T, R represents A or G, and Y represents C or T; and (ii) an equimolar mixture of the full-length complementary sequences of the different oligonucleotides set forth in (i).
 21. A combination of primers comprising: a 5′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 5; and a 3′ primer consisting of: at least 12 consecutive nucleotides of SEQ ID NO: 6; or the full-length complementary sequence of at least 12 consecutive nucleotides of SEQ ID NO:
 6. 22. A combination of primers comprising: a 3′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8; and a 5′ primer consisting of: at least 12 consecutive nucleotides of SEQ ID NO: 7; or the full-length complementary sequence of at least 12 consecutive nucleotides of SEQ ID NO:7. 